Methods and Compositions for Detection and Enrichment of Target Small RNAs

ABSTRACT

Methods and compositions are provided for detecting small target RNAs where the target RNA may be single-stranded or double-stranded and may be contained in a mixture of RNAs of different types and sizes. The methods and compositions utilize a p19 fusion protein that is capable of binding double-stranded RNA in a size-specific but sequence-independent manner and is further capable of binding to a matrix such as beads or plastic microwell plates. By labeling the p19 fusion protein or the target RNA in a polynucleotide duplex either directly or indirectly, low levels of target RNA including microRNAs can be detected from cells. This can be applied to diagnosis of pathological conditions.

BACKGROUND

Existing methods for detection of small RNAs such as small interferingRNAs (siRNAs) and micro RNAs (miRNAs) often involve multiple steps: forexample, immobilizing RNA on a filter (Northern blot), hybridizationwith a specific probe if the small RNA is a single-stranded miRNA,washing steps to remove the probe, and exposure of the filter to a film.Alternatively, small single-stranded RNAs (ssRNAs) such as micro RNAs(miRNAs) can be detected using solution hybridization of a probe to themiRNAs, RNAse treatment and gel electrophoresis to analyze themiRNA/probe product. Detection of miRNA using a DNA array requiresfluorescent-labeling of total RNA. Labeling of samples adds complexityand variability to the results. Methods that require DNA amplificationare sensitive but need corrections related to efficiency ofamplification. These methods are not appropriate for rapid diagnosticsor high throughput screening because of the multiple steps involved inthe analysis.

Evidence is accumulating that small RNAs such as miRNAs are involved inhuman disease such as neurological diseases, cardiomyopathies, andcancers (Alvarez-Garcia et al. Development 132:4653-4662 (2005)).Patterns of altered miRNA expression in tissue biopsies may serve asdiagnostic markers for these diseases. For example, the use of areliable quantitative method for detecting the differential expressionof certain miRNAs in various tumors would be valuable for diagnosis andtreatment of cancer.

SUMMARY

In an embodiment of the invention, a recombinant protein is providedhaving at least 90% sequence homology to SEQ ID NO:33, and being capableof binding a small double-stranded RNA (dsRNA). The recombinant proteinmay be additionally labeled by means of a fluorescent label, aradioactive label, a chemiluminescent label, a protein label or a smallmolecule label. In another embodiment of the invention, a DNA encodingthe recombinant protein and a vector for expressing the recombinantprotein in a host cell are provided.

In a further embodiment of the invention, a method is provided thatincludes mixing a target RNA with a p19 fusion protein capable ofbinding small dsRNA, wherein either the p19 fusion protein or the targetRNA is labeled, the label being (i) directly linked to the protein orRNA, or (ii) indirectly linked by means of a molecule capable of bindingto the p19 fusion protein or the target RNA. The method further includesimmobilizing the p19 fusion protein bound to the target RNA on a matrixfor detecting the target RNA. The detectable label is exemplified by amember of the group consisting of a fluorescent label, a radioactivelabel, a chemiluminescent label, a protein label and a small moleculelabel.

The target RNA may be an ssRNA having a size in the range of 18nucleotides to 24 nucleotides where the ssRNA hybridizes to acomplementary polynucleotide probe to form a double-stranded hybridpolynucleotide for binding to the p19 fusion protein. The complementarypolynucleotide probe may extend at the 3′ end beyond the target RNA.

The polynucleotide probe may be an RNA, a DNA or a locked nucleic acid.The target RNA may be a single-stranded molecule such as a miRNA. Thetarget RNA may be a double-stranded RNA such as an siRNA.

In an embodiment of the invention, the p19 fusion protein is immobilizedprior to binding the target RNA. Alternatively, the target RNA may beimmobilized prior to binding the p19 fusion protein. Alternatively, thep19 fusion protein may be bound to the target RNA in solution and thep19 fusion protein dsRNA complex immobilized on a matrix.

In embodiments of the invention, the matrix is a bead which may becoated with a carbohydrate or other ligand to which the p19 fusionprotein binds. The bead may be magnetic. The bead may be colored orfluorescent in a manner that differs from the label on the p19 fusionprotein or polynucleotide probe.

In an embodiment of the invention, immobilization of target RNA providesa diagnostic test for an abnormal condition in a cell in which thetarget RNA is isolated from total RNA obtained from the cell.

In an embodiment of the invention, a method is provided for detecting atarget RNA in a mixture of RNAs, such that if the target RNA is (i)single-stranded, then a complementary polynucleotide probe is added tothe mixture for forming a dsRNA and allows the dsRNA to bind to a p19fusion protein; or (ii) double-stranded, in which case dsRNA bindsdirectly to the p19 fusion protein.

In either case, one of the complementary polynucleotide probes or thep19 fusion protein is associated or linked to a label selected from afluorescent label, a radioactive label, a chemiluminescent label, aprotein label and a small molecule label.

In a further embodiment of the detection method, p19 fusion protein canbe immobilized on a matrix for binding small dsRNA and removing unboundRNA. Alternatively, small dsRNAs can be immobilized on the matrix eitherby hybridizing a target ssRNA to a matrix bound polynucleotide probe orby directly binding the target dsRNA. In this case, the p19 fusionprotein is preferably labeled.

In a further embodiment of the invention, a kit is provided thatcontains the recombinant p19 fusion protein described above,instructions for detecting a small RNA, and optionally a matrix forbinding p19 fusion protein or a polynucleotide probe. The p19 fusionprotein may be bound to a matrix in the kit. Alternatively, apolynucleotide probe may be bound to the matrix, in which case, the kitmay additionally contain a labeled unbound p19 fusion protein.

If a matrix is included in the kit, it may be a bead, for example, acolored or fluorescent bead. The bead may be coated with a carbohydratefor binding the p19 fusion protein. The bead may be magnetic.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a summary of the biogenesis of miRNAs (Esquela-Kerscher &Slack Nature Reviews Cancer 6:259-269 (2006). Transcription (1) of DNAresults in the formation of a primary miRNA (pri-miRNA) (SEQ ID NO:3).This is a dsRNA hairpin structure that is cleaved by Drosha (2), anuclear enzyme with RNase III domains to form a pre-miRNA (3). Thecleaved hairpin is transported to the cytoplasm (4) by exportin 5.Secondary cleavage occurs with Dicer (5) to generate a dsRNA of about 20to 22 bases in length. This RNA then enters the RNA-induced silencingcomplex where it is unwound to form ssRNA that hybridizes with the 3′untranslated region of the miRNA (6). The bound miRNA reduces proteinexpression either by blocking translation or causing cleavage of themiRNA (7).

FIGS. 2A-2C show properties of the molecule used for discovery ordetection of miRNA.

FIG. 2A shows a cartoon of a fusion protein consisting of amaltose-binding protein (MBP) fused to p19 which is fused to achitin-binding domain (CBD).

FIG. 2B shows a gel containing the p19 fusion protein. The figuredemonstrates that this protein can be made in large quantities.

FIG. 2C shows the crystal structure of the p19 fusion protein bound todsRNA. The view is looking down the center of the RNA helix.

FIG. 3 demonstrates that the p19 fusion protein (MBP-p19-CBD)preferentially binds dsRNA of 21 nucleotides (nt) but does not binddsRNA of 25 nucleotides or 17 nucleotides long. 0.5 μg of MBP-p19 fusionprotein bound to 30 ng of the 21-mer dsRNA in a 20 μl reaction. Thereaction also contained 30 ng of the 17-mer and 25-mer dsRNA. Lanes 1-9show use of increasing amounts of MBP-p19-CBD fusion protein (μg) andlane 10 is a size marker.

FIGS. 4A-4B show additional characterization of the p19 fusion protein.

FIG. 4A shows that 10 ng, 20 ng, 30 ng and 40 ng of dsRNA can be boundto chitin magnetic beads that contain 3 μg of the p19 fusion protein.The fusion protein is attached to the beads via the CBD. When treatedwith SDS, the dsRNA is released from the beads and can be detected onthe ethidium stained gel.

FIG. 4B shows that a small amount of dsRNA of 21 nucleotides can bepurified from a large excess of cytoplasmic RNA using p19 fusionprotein. Chitin magnetic beads with 5 pg of the bound p19 fusion proteinwere mixed with 27.5 μg of total rat liver RNA and 5 ng of 21-mer dsRNA.

-   Lane 1 shows target dsRNA prior to mixing with non-target RNA.-   Lane 2 shows the RNA that did not bind to the p19 fusion protein    chitin magnetic beads.-   Lane 3 shows 20 μl aliquot of the first 600 μl wash of the p19    fusion protein chitin magnetic beads.-   Lane 4 shows a 20 μl aliquot of the sixth 600 μl wash of the p19    fusion protein chitin magnetic beads.-   Lane 5 shows the dsRNA eluted from the beads. The top staining band    is material trapped in the well.-   Lane 6 contains a 17-mer, 21-mer and 25-mer dsRNA marker.

FIGS. 5A and 5B show a competitive gel shift assay to measure therelative affinity of RNA and DNA to the p19 fusion protein.

FIG. 5A shows binding of radiolabeled dsRNA (21 nt) to p19 fusionprotein in the presence of increasing amounts of the same unlabeleddsRNA (21 nt). Each reaction contained 16 μg of p19 fusion protein and 1ng of radioactive dsRNA.

FIG. 5B shows binding of radiolabeled dsRNA (21 nt) to fusion protein inthe presence of increasing amounts of unlabeled double-stranded DNA(dsDNA) (21 nt).

FIG. 5C shows binding of radiolabeled dsRNA (21 nt) to p19 fusionprotein in the presence of increasing amounts of unlabeled ribosomalRNA.

FIG. 5D shows binding of radiolabeled dsRNA (21 nt) to p19 fusionprotein in the presence of increasing amounts of unlabeled ssRNA (21nt).

FIGS. 6A-6B show the results of eluting 20 ng of 21 nt dsRNA from 20 μlp19 fusion protein precoated beads (containing 3 μg p19 fusion protein).

FIG. 6A shows that p19 fusion protein is stable when stored at 4° C. forat least 8 weeks such that the 21 nt RNA can be released after thespecified time.

FIG. 6B shows that 21-mer dsRNA is stable when bound to p19 fusionprotein stored at 4° C. or −20° C. The absence of RNA in the supernatentshows efficient binding of RNA. The elution demonstrates quantitativerecovery of dsRNA from p19 fusion protein beads stored for differenttimes and temperatures.

FIG. 7 shows the relative binding affinities of p19 fusion protein tovarious RNA and DNA substrates. The binding of a labeled siRNA toMBP-p19-CBD in the presence of increasing concentrations of nucleicacids described in column 1 was measured by a gel mobility shift assay.In each competitive assay, a control was included in which 50% reductionin binding of the radiolabeled 21mer siRNA was observed in the presenceof unlabeled 21mer siRNA. This was assigned a value of one. The identityof the polynucleotide, its sequence, its structure and its relativebinding affinity to MBP-p19-CBD are listed. The gaps in the structure ofthe microRNAs in 13, 14 and 15 denote mismatched base pairs.

FIG. 8 describes various approaches to labeling RNA. Radioactivelabeling is very sensitive and gives low background but is not suitablefor high throughput analysis and also has regulatory issues.Fluorescence and chemiluminescence labeling are both user friendlylabeling methods and can be used in a 96 well format with or withoutmagnetic beads and are scaleable and can be automated.

FIG. 9 shows how MBP-p19-CBD (measured in ng) when bound to fluorescentdsRNA increases flourescence polarization which can be quantitativelymeasured (mP). Fluorescence polarization is defined by the followingequation: P=(V−H)/(V+H) where P equals polarization, V equals thevertical component of the emitted light, and H equals the horizontalcomponent of the emitted light of a fluorophore when excited by verticalplan polarized light. The term mP stands for 1/1000 of the polarizationP. It is not dependent upon concentration (Lundblad et al. Mol.Endocrinol 10:607-612 (1996)).

FIGS. 10A-10B show how the p19 fusion protein can be used for discoveryof novel endogenous siRNAs.

FIG. 10A shows the results of loading 350 μg of total unc-22 RNAextracted from C. elegans onto a 20% acrylamide TBE gel. Extraction ofRNA from the gel in the 15 to 30 base pair range yields 6.1 μg of smallRNA.

FIG. 10B shows the results from binding the gel purified small RNA tothe p19 fusion protein chitin magnetic beads, washing the beads and theneluting the RNA. The mobility of the eluted RNA is indicated by an arrowat the right of the figure.

FIG. 11 shows the isolation of endogenous siRNA from a filiarialparasite D. immitis using p19 fusion protein chitin magnetic beads.50,000 fold enrichment was obtained. The mobility of the eluted RNA, inlane 9, is indicated by an arrow.

-   Lane 1 is double-stranded siRNA marker.-   Lane 2 is 10 ng of a 21mer dsRNA.-   Lane 3 is gel purified D. immitis small RNA.-   Lane 4 is gel purified RNA plus p19 fusion protein.-   Lane 5 is RNA not bound to chitin magnetic beads with p19 fusion    protein.-   Lane 6 is the first wash of the p19 chitin magnetic beads.-   Lane 7 is the result of wash 2.-   Lane 8 is the result of wash 3.-   Lane 9 is the first elution from the beads.-   Lane 10 is the second elution from the beads.

FIG. 12 shows a protocol for detecting dsRNA using biotin-labeled p19fusion protein. A polynucleotide probe (9) is covalently linked to beads(8). Small ssRNAs (tRNAs, rRNAs etc.) (10) hybridize to thepolynucleotide probe (9) to form a stable RNA hybrid on the bead (8). Abiotin-labeled p19 fusion protein (12) binds to RNA hybrids on the beads(8). The p19 fusion protein can be labeled using biotin, which can bindtightly to streptavidin (13). The streptavidin can be detected bylinkage via a second biotin molecule to an enzyme, like alkalinephosphatase or peroxidase, or by means of a fluorescent-labeled protein.Substrates for the enzyme will give a colored or fluorescent productthat can be detected with a laser. The beads to which p19 fusion proteinattaches can be identified with a laser which detects the bar codesignature of dyes. The amount of miRNA bound to a specific bead can bemeasured by the amount of p19 fusion protein bound to the beads.

FIG. 13 shows p19 fusion protein capture of dsRNA hybrid and detectionwith a miRNA specific probe. An ssRNA polynucleotide (9) labeled with(5-[(N-(3′-diphenylphosphinyl-4′-methoxycarbonyl)phenylcarbonyl)aminoacetamido]fluorescein(FAM) binds specifically to miRNA (10) in a background of total RNAincluding tRNA, rRNA and mRNA (11) to form a dsRNA that binds to a p19fusion protein (12) which is attached to a solid support, like an ELISAplate (14) or a bead for detection.

FIG. 14 shows a p19 fusion protein-based miRNA detection method. Totalcellular RNA, which includes miRNA, rRNA and mRNA (11), is hybridized toa specific probe complementary to a miRNA (9). The double-strandedmiRNA/RNA probe is then selectively and tightly bound to p19 fusionprotein (12) chitin magnetic chitin beads (8). The unbound probe can beremoved rapidly by washing the p19 fusion protein beads and thenisolating them with the aid of a magnetic rack (15). The dsRNA is theneluted from the beads in the presence of a protein denaturing agent.

FIGS. 15A and 15B show a diagnostic test for miRNAs.

FIG. 15A shows p19 fusion protein (12) attached to a bead (8) andbinding dsRNA where a single strand of the duplex is labeled with biotin(9). Streptavidin (13) is bound to the biotin and with the help of asuitable enzyme label (15) and a substrate (16), a chemiluminescent orfluorescent reaction can be initiated.

FIG. 15B shows a standard curve assay for quantifying the results fromthe detection method described in FIG. 15A. The biotin-labeled RNA probeis linked, via a streptavidin bridge, to alkaline phosphatase. Theenzyme is detected using the substrate CDP-Star, #N7001S from NewEngland Biolabs (NEB, Ipswich, Mass.), which generates light.

FIG. 16 shows a biotin-labeled ssRNA (9) immobilized on a streptavidin(13) coated solid substrate (14). Target miRNA (10) is hybridized to theimmobilized polynucleotide (9). The dsRNA is subsequently recognized andbound by a labeled p19 fusion protein (12) for detection.

FIGS. 17A-17D show the quantitative measurement of the liver specificmiRNA (miRNA122a) from rat liver total RNA.

FIG. 17A shows a non-denaturing gel with increasing amounts of syntheticmiRNA122a in picograms (pg), hybridized to 1 ng of a radioactive RNAprobe complementary to miR-122a. The dsRNA is bound to p19 fusionprotein chitin magnetic beads, washed, eluted and analyzed on a 20%non-denaturing acrylamide gel. The radioactivity is associated with themiRNA/RNA probe.

FIG. 17B shows a standard curve for miR122 that was calculated fromradioactivity eluted from the p19 fusion protein beads.

FIG. 17C shows a non-denaturing gel of miRNA/RNA probe eluted from p19fusion protein beads using a miR122 specific probe and different amountsof rat liver RNA.

FIG. 17D gives the results for 2, 5 and 10 μg of rat liver total RNAcontaining between 38 and 68 pg of miRNA122a/μg of total RNA.

FIG. 18 shows detection of Let-7 miRNA in total JURKAT cell RNA using anautoradioagraph of an acrylamide gel in which the labeled RNAcorresponds to the miRNA/RNA probe hybrid, which is shown to increaseaccording to the total RNA. A radioactive RNA probe complementary toLet-7 was hybridized to different amounts of JURKAT cell RNA, bound top19 fusion protein magnetic beads, washed and eluted. Lanes 2-4 show 2μg, 5 μg and 10 μg of total JURKAT RNA respectively.

FIG. 19 shows the DNA and amino acid sequences (SEQ ID NOS:32 and 33)for CBD-p19-MBP where MBP corresponds with amino acid 1 to 394 andnucleotide 1 to 1183, p19 corresponds with amino acid 395 to 565 andnucleotide 1184 to 1698, a polylinker corresponds with amino acid 566 to575 and nucleotide 1698 to 1726 and CBD corresponds with amino acid 576to 626 and nucleotide 1727 to 1878.

DETAILED DESCRIPTION OF THE EMBODIMENTS

Existing methods for detection of small RNAs are often complex andrequire ligation and amplification or gel electrophoresis steps. Afusion protein is described here that can be used in a simplified,sensitive and quantitative assay to detect and/or isolate small RNAs.

The fusion protein described here is exemplified by a p19 fusion proteinwhich binds a dsRNA regardless of the sequence but in a size-specificmanner, is capable of being immobilized on a substrate, and can bereadily purified.

RNAs of interest can be isolated from biological samples using the p19fusion protein. This protein may also be used to detect specificendogenous RNAs of a specific size in physiological samples that containa wide variety of RNAs normally associated with cells. The amounts ofthe RNAs of interest can be determined using quantitative assays (seefor example, FIGS. 9, 15 and 17).

Definitions

The term “small” RNA as used here and in the claims refers to RNAfragments containing or capable of forming a double-stranded region of asize of greater than about 17 nucleotides and less than about 25nucleotides, for example 21-23 nucleotides. The dsRNA may result fromtwo complementary strands in a linear duplex or a single-strandedmolecule that is folded to form a hairpin.

Where a small RNA is single-stranded, it can be hybridized to acomplementary polynucleotide probe to create either a completely dsRNAmolecule or RNA/DNA hybrid or a partially dsRNA. The RNA/DNA or RNA/DNAhybrids may include a single-stranded polynucleotide tail at one end ofthe polynucleotide probe that extends beyond the duplex regioncontaining the target RNA.

Examples of small RNAs include miRNAs, siRNAs, repeats associated RNAs(rasiRNAs). rasiRNAs are found for example in C. elegans and may preventmigration of transposons.

The “p19 fusion protein” refers to a member of the p19 family of RNAbinding proteins (Silhavy et al. Embo J. 21:3070-80 (2002) fused to oneor more additional proteins which surprisingly retains the bindingproperties of the native enzyme where the fusion protein binds smalldsRNA in a sequence-unspecific but size-specific manner (see forexample, FIGS. 2-6). The binding properties of the p19 fusion proteinwas determined for various substrates using competitive gel shiftanalysis. The results confirmed that the p19 fusion protein does notbind ssRNAs or dsDNA but does bind dsRNA in a size specific manner (FIG.7).

P19 proteins are highly conserved in Tombus plant viruses. Relatedproteins have been isolated from many plant viruses such as CarnationItalian ringspot virus p19 (NP 612584), Tomato bushy stunt virus(CAC01278), Artichoke mottled crinkle virus (NP 039812), Lettucenecrotic stunt virus (CAC01267), Lisianthus necrosis virus (CAM98056),Grapevine Algerian necrosis virus (AAX76895), Cucumber necrosis virus(CAC01089), Pelargonium necrotic spot virus (NP 945118), CucumberBulgarian virus (AA033943), Maize necrotic streak virus (AAG21219), Pearlatent virus (AAM49806), Grapevine Algerian latent virus (AAX76895), andCymbidium ringspot virus (CAA33535) (accession numbers in parenthesis).

The p19 proteins described above includes a fusion to one or moreproteins where at least one of the proteins has a size greater than 10amino acids. Examples of proteins for fusion to p19 includecarbohydrate-binding proteins exemplified by MBP, CBD andcellulose-binding domain; enzymes such as O6-alkylguanine-DNAalkyltransferase (U.S. Patent Applications 2006/0292651; 2006/0024775;2004/0115130; 2007/0082336; 2007/0207532; 2007/0243568) or luciferasethat are capable of responding to a substrate to produce fluorescence ora detectable color signal; enzyme substrates such as biotin; antibodies;and protein epitopes.

A “polynucleotide probe” refers to a ssDNA, ssRNA or a locked nucleicacid that may be synthetic and is complementary at least in part to thetarget RNA if the target RNA is single-stranded (Vester & WengelBiochemistry 43(42):13233-41 (2004)). The probe may be labeled.Alternatively, the probe is not labeled and is used in an assay in whichthe p19 fusion protein is or becomes labeled during the assay.

Methods of Making p19 Fusion Proteins

The formation of fusion proteins can be readily achieved using DNAvectors available in the art such as those described in the New EnglandBiolabs (NEB, Ipswich, Mass.) catalog. Example 1 which is not intendedto be limiting describes a method of making a p19 fusion protein fromCarnation Italian ring spot virus in which the protein is fused at theamino end to an MBP, which permits purification of the protein, and atthe carboxy end to the CBD, for tightly binding the magnetic chitinbeads (FIG. 2).

Labeling the p19 Fusion Protein or Polynucleotide Probe

Labeling a target molecule may be achieved either directly or indirectlyby labeling a molecule capable of binding the target molecule. Theselabels may be attached to a reagent polynucleotide probe for binding thetarget RNA, or to the p19 fusion protein. Any suitable label known inthe art can be used such as a radioactive label (for example, ³²P), afluorescent label, a chromogenic label such as phycoerythrin, an enzymelabel or a modified base for reacting with an enzyme(biotin-strepavidin).

Examples of methods of detection using fluorescent labels include FAM.Another method is Fluorescence Resonance Energy Transfer (FRET). Thisinvolves two different fluorescent molecules (or proteins), one forlinking to the p19 fusion protein and the other for linking to the RNAprobe. When the dsRNA binds to the p19 fusion protein, the two moleculesare in close enough proximity for efficient energy transfer to generatea fluorescent signal. This method does not require removal of theunbound RNA probe and is therefore suitable for large scale screening.Another method is Fluorescent Polarization (FP) where the two subunitsof the MBP-p19-CBD protein are about 10× the molecular weight of the17-25 base-paired dsRNA. This difference in size between the bound andunbound RNA can be detected by FP. Another method is quantum dotanalysis such as described by Yezhelyev et al. J Am Chem Soc.130(28):9006-12 (2008)), which may also be used for detection of dsRNAs.

Examples of enzyme labels include methods in which for example aluciferase, green fluorescent protein or alkyl guanine DNA alkyltransferase are used. Small molecules such as biotin may be used. Biotinis linked to the polynucleotide probe, and avidin-bound enzymes, likehorseradish peroxidase or alkaline phosphatase react with biotin throughstreptavidin to signal the presence of a molecule of interest. This is astandard method for ELISA detection of antibodies.

Immobilization of Reagents

The target RNA may be immobilized either directly or indirectly on or ina matrix. Indirect immobilization of the target RNA may occur by meansof (a) hybridizing a target ssRNA to a matrix bound polynucleotide probeto form a small dsRNA which is subsequently recognized by a p19 fusionprotein in solution; or (b) binding small dsRNA to p19 fusion proteinbound to a matrix; or (c) binding dsRNA with p19 fusion protein insolution and then binding the complex to a matrix.

The p19 fusion protein can be readily immobilized on a matrix if thatsolid substrate is coated with a molecule with which the fusion proteinbinds, for example, chitin for binding chitin-binding domain or amylosefor binding MBP. A polynucleotide probe can be bound to a matrix bymeans of a ligand such as biotin.

Examples of matrices include beads, columns, microtiter plates, a chip,or other 2-dimensional or three-dimensional formats known in the art. Inaddition, channels coated with chitin in microfluidic devices may beused to immobilize RNAs of interest.

Sensitivity of the Assay

Levels of enrichment of dsRNA of any sequence having a size preferablyof greater than 17 nucleotides and less than 25 nucleotides can beachieved of greater than 20,000 fold and as much as 100,000 fold fromtotal RNA. Moreover, as little as 10 pg of miRNA can be detected in amillion-fold excess of total RNA and 50 pg of miRNA can be measured intotal cell RNA from a tissue. Competitive gel shift data demonstratethat neither unbound single-stranded probe nor cytoplasmic RNA blocksbinding of a miRNA and RNA probe in a p19 fusion protein detectionassay.

Uses of the Assay

A specific polynucleotide probe may be attached to a substrate such as aplate or beads using standard methodology (for examplebiotin-steptavidin labeling) and exposed to a cell lysate from, forexample, a biopsy. Only ssRNA of a specific sequence contained in thecell lysate will bind the immobilized polynucleotide probe. Labeled p19fusion protein may then bind to the dsRNA or RNA/DNA hybrid and can bedetected. FIGS. 17 and 18 demonstrate the feasibility of this approachfor the quantitative detection of mir122a miRNA in total RNA extractfrom rat liver. Examples 4 and 5, FIGS. 17 and 18 illustrate howradioactive labeling or fluorescent-labeling is effective in detectingsmall amounts of the target miRNA in total lysate.

The labeled p19 fusion protein may either be in solution and optionallysubsequently immobilized or already immobilized on a coated matrix (forexample, chitin) where for example, the matrix is magnetic beads or thewell of a microtiter plate. Accordingly, unbound material can be removedand the target RNA can be subsequently eluted from the matrix foranalysis.

This approach can be adapted for high throughput screening of samplesfor target miRNAs (FIG. 14). Automation of detection can be facilitatedusing magnetic beads. For example, a biotinylated probe, previouslyhybridized to a miRNA target, can be linked to a plate coated withstreptavidin. In this way, a labeled p19 fusion protein provides asignal for detecting miRNA (FIG. 16).

In an embodiment, automation of detection for high throughput processingof samples is facilitated by scanning an ELISA plate for binding ofmodified p19 fusion protein with labeled double-stranded miRNA. TheELISA plate can be coated with chitin to which p19-CBD fusion proteinsbind. The unbound RNA can be removed by washing the plate and theremaining bound RNA can be detected by means of the attached probe. Ifthe probe contains biotin, then it can be linked to a chromogenicreadout using avidin conjugated to alkaline phosphatase or horseradishperoxidase (FIG. 15). An ELISA plate format for miRNA detection has manyadvantages. There exists an extensive amount of instrumentation forwashing, reading and handling of ELISA plates. High throughput analysisis an important feature of analyzing clinical samples.

The methods and compositions described herein may be used toquantitatively determine the presence and amounts of endogenous miRNAsfor purposes that include diagnosis or analyzing a wide range ofpathologies such as cancers including determining the tissue of originof the metastasized cancer, neuropathologies, and pathologies in otherorgans. These methods provide rapid, cost effective, efficient andscaleable detection of miRNAs in vitro.

All references cited above and below, as well as U.S. provisionalapplication Ser. No. 60/983,503 filed Oct. 29, 2007, are incorporated byreference.

Examples Example 1 Cloning of the D19 Fusion Protein and Binding toSize-Specific dsRNA

The p19 protein from the Carnation Italian ringspot virus codes for a 19kDa protein and has a binding preference for 17-25 by RNAs (Vargason etal. Cell 115:799-811) (2003)).

Sequence of the p19 protein from the Carnation Italian ringspot virus isas follows:

(SEQ ID NO: 1) 1 MERAIQGNDT REQANGERWD GGSGGITSPF KLPDESPSWT EWRLYNDETNSNQDNPLGFK 61 ESWGFGKVVF KRYLRYDRTE ASLHRVLGSW TGDSVNYAAS RFLGANQVGCTYSIRFRGVS 121 VTISGGSRTL QHLCEMAIRS KQELLQLTPV EVESNVSRGC PEGIETFKKE SE

The plasmid vector pMAL-c2G from New England Biolabs (NEB, Ipswich,Mass.), was cleaved with PstI and HindIII, within the multiple cloningsite. The following two PCR primers were used to amplify thechitin-binding domain, CBD, from the plasmid pTYB1 from New EnglandBiolabs (NEB, Ipswich, Mass.): 5′ G ACT CTG CAG ACG ACA AAT CCT GGT GTATCC GCT 3′ (SEQ ID NO:34) CBD (PstI) forward primer and 5′ T AGG AAG CTTTCA TTG AAG CTG CCA CAA GGC AGG AAC 3′ (SEQ ID NO:35) CBD (HindIII)reverse primer. After amplification the PCR product was cleaved with PstI and Hind III and cloned into the plasmid pMAL-c2G. The new vector wasthen cleaved with BamHI. The p19 fusion protein coding sequencing,accession number NC 003500, was amplified with two primers containingBamHI sites. The PCR products was cleaved with BamHI and then clonedinto the MBP CBD vector described above. The resulting plasmid constructcoded for a fusion protein that contained an amino terminal MBP and acarboxy terminal CBD.

The MBP-p19-CBD fusion protein was isolated in high yields by bindingand elution from amylose resin. The fusion protein was shown to befunctionally active as described below.

The MBP-p19-CBD fusion protein (FIG. 19) was shown to bind an siRNA in asize-dependent sequence-independent manner where the size was preferablygreater than 17 nucleotides and smaller than 25 nucleotides. (FIG. 3) Itwas concluded that the presence of a large, 42 kDa, fusion partner likeMBP does not have a major effect on siRNA binding to p19 fusion protein(FIG. 2).

The affinity of the p19 fusion protein for different substrates wasdetermined by gel shift analysis (FIGS. 5 and 7). The affinity of p19fusion protein was greater for siRNAs than for miRNAs which containedmismatched base pairs. The p19 fusion protein bound to 21-mer dsRNA/DNAhybrid but not to dsDNA of the same size or ssRNA, single-stranded DNAor ribosomal RNA. Binding of RNA to p19 was also detected byfluorescence-polarization studies that used fluorescent-labeled RNA(FIGS. 5, 7 and 9).

The MBP-p19-CBD fusion protein was used for siRNA isolation (FIGS. 12and 13). Small RNAs that bound to the p19 fusion protein were purifiedwith chitin magnetic beads. The CBD portion of the p19 fusion proteinattached the dsRNA:protein complex to the beads (FIGS. 14 to 16).Background binding could be reduced with the addition of bovine serumalbumin (BSA). The small RNAs were eluted from the chitin beads bydenaturing the protein with 0.5% SDS.

In a reconstruction experiment, a defined amount of siRNA was added tototal rat liver RNA, bound to p19 fusion protein, concentrated withchitin magnetic beads and eluted. Greater then 5,000× enrichment wasobtained using this approach (FIGS. 3 and 4).

Example 2 Determination of the Sensitivity and Quantification of theDetection Method for RNAs using p19 Fusion Protein and LiquidScintillation

A method was developed using ³²P-labeled polynucleotide probes to detectand quantify the abundance of endogenous miRNA in a total RNA sample.The p19 fusion protein specifically detected a hybrid between a miRNAand a labeled radioactive RNA probe in a one million-fold excess ofcytoplasmic RNA. This was demonstrated using the abundant liverspecificmiRNA, miR122a. A standard curve was made using increasing amounts ofsynthetic miR122a mixed with a large excess of JURKAT total RNA (Tlymphocyte cell) to mimic assay conditions. JURKAT cell total RNA didnot contain any detectable miR122a by this method. Variable amounts ofmiR122a oligo were hybridized to a constant amount or radioactive RNAprobe, which was complementary to miR122a. A background standard lackingany added miR122a oligo was processed in the same as the samples (FIG.17).

A quantitative measurement of endogenous miR122a was made by incubatingrat liver total RNA with the miR122a specific probe. Three assays withdifferent amounts of rat liver total RNA were performed to ensureconcordance of the results. After hybridization, each sample wasincubated with p19 fusion protein-coated magnetic beads to allow forbinding of the miR122a-probe duplex. To remove the unbound RNA, p19fusion protein beads were washed 5 times and the miR122a duplex waseluted from the beads by denaturing p19 fusion protein with an elutionbuffer containing 0.5% SDS. The eluted radioactive duplex was countedand the background control was subtracted from each sample. Todemonstrate that the radioactivity corresponded to the miR122a/probe,the eluent was loaded on an acrylamide gel (FIG. 5A) and exposed toX-ray film. As observed on the autoradiograph, the eluted RNA wasdouble-stranded, not single-stranded probe.

After subtracting the control radioactive count from each result, thestandard counts corresponding to the miR122a duplex were plotted as afunction of synthetic miR122a amount (FIG. 5B). A linear curvedemonstrated the proportionality between the radioactive signal and theamount of miR122a complex. Comparison to the standard curve provides arelative measurement of the miR122a abundance in a physiological sample(FIGS. 5C and 5D). A value of 50 pg +/−12 pg of miR122a per μg of ratliver total RNA was obtained for the three concentrations of RNA. Thedetection is linear over two orders of magnitude and has a sensitivityof 2-5 pg of miRNA.

(a) Labeling miR122a Probe using γ-³²P-ATP

In a microfuge tube, 300 ng of miR122a probe (5′OH-aacaccauugucacacuccaua) was added to 2 μL of T4 polynucleotide kinasereaction buffer (70 mM Tris-HCl (pH7.6), 10 mM MgCl2, 5 mMdithiothreitol from New England Biolabs (NEB, Ipswich, Mass.)) and 3 μLof miliQ water. Then, 10 μL of γ-³²P- ATP (PerkinElmer, Waltham, Mass.)at 6,000 Ci/mmol and 2 μL of T4 polynucleotide kinase (10,000 units/mL)from New England Biolabs (NEB, Ipswich, Mass.) were added to thelabeling reaction. The reaction tube was placed in a 37° C. heat blockfor 40 to 60 minutes, and then the reaction was stopped by inactivatingthe enzyme at 65° C. for 20 minutes. After stopping the reaction, theentire labeling reaction was loaded onto a CentriSep column (PrincetonSeparation, Freehold, N.J.) and centrifuged for 2 minutes at 3,000 rpmto remove the excess γ-³²P-ATP. The specific activity of labeled probewas determined by counting 1 μL of a ten-fold dilution of the purifiedlabeling reaction in a scintillation counter.

(b) Total RNA Extraction from JURKAT Cells

JURKAT total RNA was obtained using Trizol (Invitrogen, Carlsbad,Calif.) as recommended by the manufacturer. 10 mL of Trizol were addedto the JURKAT cell pellet. The sample was transferred in a 30 mL tubeand cells were disrupted by homogenization using a syringe. Aftercomplete homogenization, the tube was incubated 5 minutes at roomtemperature to permit the complete dissociation of nucleoproteincomplex. 2 mL of chloroform was added to the sample, vortexed for 15seconds and incubated at room temperature for 2 to 3 minutes andcentrifuged at 4° C. for 15 minutes at 12,000 g. To precipitate the RNAsample, the aqueous phase was transferred to a new tube containing 5 mLof isopropanol, placed at room temperature for 10 minutes andcentrifuged at 4° C. for 10 minutes at 12,000 g. The RNA pellet was thenwashed with 10 mL 75% ethanol and thoroughly drying. The pellet wasresuspended with 200 μL of sterile Tris-EDTA. The total RNAconcentration was estimated via optical density using the nanodropspectrophotometer and the purity was evaluated by the ratio A260 nm/A280nm.

(c) Assay for Small RNAs

RNA samples were added to loading buffer and loaded into pre-rinsedwells of a TBE Gel 20% acrylamide (Invitrogen, Carlsbad, Calif.) as wellas the RNA size marker (siRNA Marker, New England Biolabs (NEB, Ipswich,Mass.)). After running at 100V for 2 hours, the gel was stained withSybrGold (Invitrogen, Carlsbad, Calif.) and visualized on a fluorimager.In the competitive binding assays of RNA/DNA to p19 fusion protein, thegels were exposed to X-ray film and the bands scanned to determinerelative binding affinities.

(d) Quantification of Endogenous miR122a using p19 Fusion Protein-BasedLiquid Scintillation miRNA Detection Method

Quantification of sensitivity was determined by (1) varying amounts oftotal rat liver RNA (2, 5 and 10 μg) incubated with 1 ng of specificprobe; and (2) varying amounts of miR122a RNA (target RNA) (500 pg to0.32 pg).

A miR122a complementary sequence was synthesized and labeled with aradioactive label. Specifically, 5′ γ-³²P aacaccauugucacacuccaua (SEQ IDNO:2) was labeled at the 5′ end using γ-³²P-ATP. Incubation wasperformed 2 hours at 65° C. in 1× p19 fusion protein binding buffer (20mM Tris HCl, 100 mM NaCl, 1 mM EDTA and 1 mM TCEP, pH 7 at 25° C.). Thelabeled probe was mixed with miR122a RNA and total JURKAT RNA andincubated for 2 hours at 65° C. to allow hybridization between thetarget miR122a and the probe.

Hybridized dsRNA was allowed to bind to p19 fusion protein coated beads.These beads were made as follows: Chitin magnetic beads (NEB#E8036) werepretreated with BSA by washing the beads in 1× BSA buffer (20 mM TrisHCl, 100 mM NaCl, 1 mM EDTA, 1 mM TCEP and BSA at 1 mg/mL pH 7 at 25°C.) twice using a magnetic rack (New England Biolabs #S1506S (NEB,Ipswich, Mass.)) and resuspended in the same buffer and incubatedovernight at 4° C. p19 fusion protein-bound magnetic beads were made bymixing p19-CBD fusion protein with pretreated chitin beads (30 μg p19fusion protein for 200 μl beads suspension) in 200 μL 1× p19 fusionprotein binding buffer with 1 mg/mL BSA and incubated at 4° C.overnight. The subsequent protein beads were stored at 4° C.

Binding of miR122a-probe duplex to p19 fusion protein occurred when 10μL of the p19 fusion protein-coated magnetic beads were incubated for1.5 hours at room temperature in an orbital shaker in 1× p19-bindingbuffer containing RNAse inhibitor and BSA at 1 mg/mL. Unbound RNA waseliminated by washing the beads 5 times with 500 μL 1× p19 fusionprotein wash buffer prewarmed at 37° C. (20 mM Tris HCl, 100 mM NaCl, 1mM EDTA and 1 mM TCEP, pH 7 at 25° C.) shaking for 5 minutes at roomtemperature.

miR122a-probe duplex was eluted from the beads with 20 μL of 1× p19fusion protein elution buffer (20 mM Tris HCl, 100 mM NaCl, 1 mM EDTAand 0.5% SDS, pH 7 at 25° C.) after incubation 10 minutes at 37° C.followed by mixing 10 minutes at room temperature. The beads were spundown and the supernatant was removed. 18 μL of the elution were loadedon 20% acrylamide gel (Invitrogen, Carlsbad, Calif.) using TBE bufferand 2 μL of the eluted RNA were used for radioactive counting. Theresults are shown in FIG. 17.

(e) Qualitative Detection of Let-7a using p19 Fusion Protein-BasedLiquid Scintillation miRNA Detection Method

miRNA Let-7a was detected in JURKAT total RNA as follows: Three sampleswere prepared containing different amounts of JURKAT total RNA. JURKATtotal RNA was incubated with the Let-7a specific probe to allowhybridization between the target and probe. The probe was a syntheticLet-7a complementary sequence labeled at the 5′end using γ-32P-ATP.After hybridization, the three samples containing the potential Let-7acomplex were incubated with p19 fusion protein-coated beads.

To remove the unbound RNA and the excess single-stranded probe, p19fusion protein coated beads were washed 5 times and the Let-7a complexwas eluted from the beads by denaturing p19 fusion protein with anelution buffer containing 0.5% SDS. The radioactivity in each sample wasmeasured using liquid scintillation counting. To ensure that theradioactive count corresponded to the signal of the Let-7a duplex, therest of the elution was separated and autoradiographed (FIG. 7).

The results confirmed that Let-7a miRNA was present in the JURKAT cellline at detectable levels by gel electrophoresis and scintillationcounting.

Different samples containing various amount of JURKAT total RNA wereincubated with 600 pg of a specific RNA probe (synthetic Let-7acomplementary sequence, 5′ γ-³²P-cuauacaaccuacuaccucaaa) (SEQ ID NO:2)labeled at the 5′end using γ-³²P-ATP. Incubation was performed for 2hours at 65° C. in 1× p19 fusion protein binding buffer (20 mM Tris HCl,100 mM NaCl, 1 mM EDTA and 1 mM TCEP, pH 7 at 25° C.) to allowhybridization between the target Let-7a and the RNA probe. In order forthe p19 fusion protein-coated beads to recognize the Let-7a-probeduplex, the solution containing miRNA duplex was incubated with p19fusion protein beads (from 10 μL of a suspension of p19 fusion proteincoated beads) for 1.5 hours at room temperature in 1× p19 fusion proteinbinding buffer containing RNAse inhibitor and BSA at 1 mg/mL. UnboundRNA was eliminated by washing the beads 5 times with 500 μL 1× p19fusion protein wash buffer pre-warmed at 37° C. (20 mM Tris HCl, 100 mMNaCl, 1 mM EDTA and 1 mM TCEP, pH 7 at 25° C.) shaking for 5 minutes atroom temperature. The Let-7a-probe duplex was eluted from the beads with20 μL of 1× p19 fusion protein elution buffer (20 mM Tris HCl, 100 mMNaCl, 1 mM EDTA and 0.5% SDS, pH 7 at 25° C.) after incubation 10minutes at 37° C. followed by mixing 10 minutes at room temperature. Thebeads were spun down and the supernatant was removed. 18 μL of theelution were loaded on TBE 20% acrylamide gel (Invitrogen, Carlsbad,Calif.) and 2 μL were used for radioactive counting. The results areshown in FIG. 18.

(f) Binding of p19 Fusion Protein to miRNA/RNA PolyA-Tail Probe

To improve the sensitivity of detection, p19 fusion protein binding to amiRNA hybridized to a longer RNA probe was tested. Synthetic miR122a washybridized to a FAM-labeled probe containing a 20 to 30 base polyA-tail. The hybrid obtained was incubated with p19 fusion protein andseparated by PAGE electrophoresis and stained by SybrGold (Invitrogen,Carlsbad, Calif.). A mobility shift was observed when the hybrid wasincubated with the p19 fusion protein. No shift was observed in thesample without p19 fusion protein. This result demonstrated that p19fusion protein binds a miRNA/RNA polyA-tail probe (FIG. 8) and may beused in future detection methods. An increase in the length of thepolynucleotide probe allows for increased sensitivity of detection.

10 ng of synthetic miR122a was hybridized to 10 ng of probe containing anon-radioactive 3′ polyA-tail (5′ P-aacaccauugucacacuccaua-polyA tail)(SEQ ID NO:2) at 65° C. for 10 minutes. The hybrid obtained wasincubated with 1.5 μg of p19 fusion protein (New England Biolabs (NEB,Ipswich, Mass.)) at room temperature for 1.5 hours in binding buffer (20mM Tris HCl, 100 mM NaCl, 1 mM EDTA, 1 mM TCEP, pH 7 at 25° C.), toallow binding. A sample without p19 fusion protein was performed inidentical condition as a control. The two samples were loaded on 20%acrylamide gel in TBE buffer (Invitrogen, Carlsbad, Calif.) and stainedby SybrGold (Invitrogen, Carlsbad, Calif.).

Example 3 A D19 Fusion Protein-Based RNA Detection Method using aFluorescent-Labeled Polynucleotide Probe

A standard curve using a synthetic FAM-labeled RNA probe (FIG. 9)complementary to miR31 was created. A background standard withoutsynthetic miR31 was processed in a similar way. The hybridization stepwas performed in presence of a large excess of JURKAT total RNA. JURKATcells do not have miR31. Each sample was processed in triplicate toensure concordance of the results. After hybridization, each sample wasincubated with p19 fusion protein-coated magnetic beads to allowrecognition between miR31-probe duplex and p19 fusion protein protein.To remove unbound RNA, p19 fusion protein beads were washed twice andthe miR31 duplex was eluted from the beads by denaturing p19 fusionprotein with an elution buffer containing 0.5% SDS. Fluorescence of thesamples was read with an excitation wavelength of 485 nm, an emissionwavelength of 520 nm and a cutoff of 495 nm. The background signal wassubtracted from each standard to remove the signal due to non-specificbinding to the beads. For each triplicate, we calculated the average andstandard deviation. The average of standard Relative Fluorescence Unit(RFU) corresponding to the miR31 duplex was plotted as a function ofsynthetic miR31. A linear graph demonstrated the proportionality betweenthe fluorescent signal and the amount of the miR31 complex.

To increase the sensitivity and reduce the variability, each componentof the buffer was analyzed to determine which reagents might cause ashift or a quenching of the specific fluorescence signal. To reduce thefluorescent background, each buffer and sample were maintained in theabsence of UV absorbing compounds and dust. Excitation scans obtaineddemonstrated that the [tris(2-carboxyethyl)phosphine] (TCEP) containedin each buffer quenched the fluorescent signal (FIG. 11A). Unmodifiedbinding buffer absent TCEP and BSA (20 mM Tris-HCl, 100 mM NaCl, 1 mMEDTA, pH 7.0 at 25° C.) was used. Sensitivity tests were performed todefine the best conditions for optimal sensitivity. The sensitivity washigher when the miRNA was in an elution buffer containing 0.1M NaOH(detect 5 pg) compared with an elution buffer containing SDS 0.5%(detect 40 pg) (FIG. 12). Elution of the miRNA complex from the p19fusion protein beads was performed using an alkaline buffer containing0.1 M NaOH.

Fluorescence of the samples was read with an excitation wavelength of492 nm, an emission wavelength of 520 nm and a cutoff of 515 nm. Thebackground signal was subtracted from each sample. Reactions were intriplicate. The average of standard Relative fluorescence units (RFU)corresponding to the miR31 duplex was plotted as a function of syntheticmiR31 amount. The detection is linear. The variability of the detectionprotocol was markedly reduced in alkaline buffer with a detection limitof 10 pg compare to 5 ng for the previous experiment suggesting reducedfluorescence background and a higher sensitivity of detection.

1. A recombinant protein having at least 90% sequence homology to SEQ IDNO:33 and capable of binding a 21 nucleotide double-stranded RNA(dsRNA).
 2. The recombinant protein according to claim 1, furthercomprising: a detectable label selected from a fluorescent label, aradioactive label, a chemiluminescent label, a protein label and a smallmolecule label.
 3. A DNA encoding the protein of claim
 1. 4. A vector,comprising: the DNA of claim 3 for expressing the recombinant protein ina host cell.
 5. A method; comprising: mixing a target RNA with a p19fusion protein, wherein either the p19 fusion protein or the target RNAis labeled, the label being (i) directly linked to the protein or targetRNA, or (ii) indirectly linked by means of a molecule capable of bindingto the p19 fusion protein or target RNA; and immobilizing on a matrixthe p19 fusion protein bound to the target RNA for detecting the targetRNA.
 6. A method according to claim 5, wherein the target RNA is asingle-stranded RNA (ssRNA), the ssRNA hybridizing to a complementarypolynucleotide probe to form a double-stranded hybrid polynucleotide forbinding to the p19 fusion protein.
 7. A method according to claim 6,wherein the complementary polynucleotide probe is an RNA, a DNA moleculeor a locked nucleic acid.
 8. A method according to claim 6, wherein thecomplementary polynucleotide probe extends at the 3′ end beyond thetarget RNA.
 9. A method according to claim 6, wherein thesingle-stranded molecule is an miRNA.
 10. A method according to claim 5,wherein the target RNA is a dsRNA.
 11. A method according to claim 10,wherein the dsRNA is an siRNA.
 12. A method according to claim 5,wherein the p19 fusion protein is immobilized prior to binding thetarget RNA.
 13. A method according to claim 5, wherein the target RNA isimmobilized prior to binding the p19 fusion protein.
 14. A methodaccording to claim 5, wherein the detectable label is selected from thegroup consisting of a fluorescent label, a radioactive label, achemiluminescent label, a protein label and a small molecule label. 15.A method according to claim 5, wherein the p19 fusion protein is boundto the target RNA to form a complex which is then immobilized on amatrix.
 16. A method according to claim 5, wherein the matrix has acolored or fluorescent label that differs from the label on the p19protein or polynucleotide probe.
 17. A method according to claim 5 or16, wherein the matrix is a bead.
 18. A method according to claim 17,wherein the bead is magnetic.
 19. A method according to claim 17,wherein the bead is coated with a carbohydrate to which the p19 fusionprotein can bind.
 20. A method according to claim 5, wherein theimmobilized target RNA is diagnostic for an abnormal condition of acell.
 21. A method according to claim 5, wherein the target RNA isdiagnostic of an abnormal host cell and is present in a mixturecomprising a plurality of types and sizes of RNA.
 22. A method fordetecting a target RNA in a mixture of RNAs, such that if the target RNAis (i) single-stranded, adding a complementary polynucleotide probe forforming a dsRNA and allowing the dsRNA to bind to a p19 fusion protein;or (ii) double-stranded, binding the dsRNA directly to the p19 fusionprotein, wherein either the complementary polynucleotide probe or thep19 fusion protein is linked to a label selected from a fluorescentlabel, a radioactive label, a chemiluminescent label, a protein labeland a small molecule label.
 23. A method according to claim 20, furthercomprising: immobilizing the p19 fusion protein on a matrix for bindinglabeled dsRNA and removing unbound RNA.
 24. A method according to claim20, further comprising: immobilizing the dsRNA on a matrix and binding alabeled p19 fusion protein to the dsRNA.
 25. A kit, comprising: therecombinant protein in claim 1, instructions for detecting a small RNA,and optionally a matrix for binding p19 fusion protein or apolynucleotide probe.
 26. A kit according to claim 25, wherein the kitcontains a matrix and the p19 fusion protein is bound to the matrix. 27.A kit according to claim 25, wherein the kit contains a matrix and thematrix further comprises one or more polynucleotide probes; and therecombinant p19 fusion protein is labeled.
 28. A kit according to claim25, wherein the matrix is a bead.
 29. A kit according to claim 25,wherein the bead is colored or fluorescent.
 30. A kit according to claim27, wherein the bead is magnetic.
 31. A small RNA, comprising a 21nucleotide dsRNA.